IGV-X 2.19.5-igvx.3

Bug-fix and polish release on top of v2.19.5-igvx.2.

Highlights

• Quiet, configurable update checks - startup update checks are silent when you are already current; new Help > Update Settings... dialog (Daily / Weekly / Never) controls check frequency.
• Graceful handling of retired Broad sample data - degrade cleanly when Broad-hosted sampleinfo data is unavailable instead of failing hard.

Packaging

Built with the native jpackage launcher (arm64). Info.plist document-type patch hardened: typed PlistBuddy Add + fail-fast verification so Finder session-file associations are always present in release builds.

SHA256:

• IGV-X-2.19.5-igvx.3.dmg: d66c2659dc0ff5bcfd2ac36878efc4445db0d1711e89cfc9377c347005df4dea
• IGV-X-2.19.5-igvx.3.zip: 778662c315a07be72700273499ad0e32d16abc6102668be3c7ffa10700c9407e

Unchanged from .2: bundled TAIR10 plant genome, Finder session-file association (double-click .igvx opens IGV-X), undo/redo for tracks and genome loads, high-quality export, recent-files history.

IGV-X v2.19.5-igvx.2

IGV-X v2.19.5-igvx.2 — Release Notes

IGV-X is a customized version of IGV built specifically for
micropeptide's research — Arabidopsis
epigenetics, whole-genome bisulfite sequencing (WGBS) methylation analysis,
and large multi-track sessions. It is designed
around those workflows while remaining fully compatible with standard IGV
sessions and genomics file formats.

IGV-X is a robust, modern fork of the Integrative Genomics Viewer (IGV)
(upstream fork base: 2.19.X stable, commit e2bcf4200). It is fully compatible
with standard IGV sessions and genomics file formats, and adds a hardened
chromosome-name resolution layer, large-session performance work, and a
modernized macOS experience.

New in this release

First-run update setup + automatic update checks

• On first launch, IGV-X asks whether you want it to check for updates from
  micropeptide's GitHub releases automatically, and how often:
  once a day, once a week, or never (manual only).
• When automatic checking is enabled, IGV-X quietly checks on the chosen
  schedule and only notifies you when a new version is actually available.
• The interval is configurable in Preferences > Updates (IGV-X) —
  "Automatic update check interval in hours".

About IGV-X

• The About dialog now names the customization: "A customized version of IGV
  built specifically for micropeptide's research (Arabidopsis epigenetics /
  WGBS)" with a pointer to Help > Check for Updates.

In-app updates (from v2.19.5-igvx.1)

In-app updates (GitHub release channel)

• Help > Check for Updates... — IGV-X checks Micropeptide/IGV-X releases
  on GitHub for a newer version and offers a one-click download of the new
  .dmg installer.
• Optional startup check (off by default): Preferences > Updates (IGV-X) >
  "Check for updates on startup".
• Version comparison understands the vX.Y.Z-igvx.N release scheme.

Highlights of the IGV-X fork

Chromosome-name resolution (top priority)

• Fixes the stock IGV 2.19.5 bigWig NullPointerException on TAIR10 WGBS
  sessions: BBFile.getIdForChr() returning null when hundreds of
  methylation bigWigs use Chr1..ChrM against a RefSeq-aliased genome.
  Missing mappings never NPE — they degrade gracefully and diagnose
  honestly.
• Case-insensitive, alias-aware chromosome resolution across bigWig/bigBed/
  BAM/BED/VCF: Chr1/chr1/CHR1/1/RefSeq accessions/organellar names,
  using genome alias information — never global lowercase conversion,
  never renaming user files.
• Tools > Diagnose Track/Session... shows exactly how each file's
  chromosomes compare to the loaded genome (exact / case-only / alias-only /
  missing), plus index and resource checks.

Large-session performance (~900 bigWigs)

• Bounded loading threads, async track loading with honest progress, viewport
  culling, and caching — no more freezing the UI while a big session loads.

Sessions & files

• Relative session paths by default (relative to the session file).
• Optional .igvx.json companion metadata; sessions still load if it is missing.
• Unified smart Open (files + sessions auto-detected) and recent files.
• Cancel Session Loading — escape a stuck session load and open another.
• Unsaved-session close confirmation.
• Bookmarks & gene-region highlights persisted in the session file.
• Batch track import: File > Open Folder of Tracks... scans subfolders,
  filters by type, multi-select.
• Arabidopsis (tair10) gene lists — DNA methylation core, RdDM pathway,
  small RNA machinery, histone marks & readers, imprinting/DME, flowering time
  (every AGI verified against TAIR10 GTF).

Navigation & region selection

• Trackpad two-finger swipe / Magic Mouse pan (configurable sensitivity),
  without breaking vertical scroll.
• ROI drag-select, multi-track selection (Cmd/Shift-click), data-panel
  selection highlight.
• Configurable default quantitative-track ranges (e.g. min -5 / max 100)
  in Preferences > Tracks > Default Quantitative Range (IGV-X).

Organize tracks by genotype

• Tracks > Organize Tracks by Genotype... — group tracks by genotype with
  per-genotype background tint, then order CG → CHG → CHH inside each group
  with consistent context colors across genotypes. Editable, remembered
  rules; optional auto-organize after session/batch loads.

Export

• High-quality PNG / SVG / PDF export (publication mode, selected tracks
  only, DPI control).

Diagnostics & error recovery

• Exception dedup / rate-limiting (per-type 60 s cooldown) so repeated errors
  don't spam.
• Batch command listener preserved (port 60151: new/genome/load).

macOS app

• Native system menu bar, fullscreen, standard shortcuts, Dock icon,
  window-state memory, accessible dialogs, Retina/HiDPI, information-dense
  dark-friendly UI. App name is IGV-X, own bundle ID, prefs/caches/logs
  separated from stock IGV (~/igvx). Bundled JDK — no Java install needed.

Downloads

• IGV-X-2.19.5-igvx.dmg — shareable installer (drag to Applications)
• IGV-X-2.19.5-igvx.zip — same app, zip form
• SHA256SUMS + version.txt

Compatibility

Standard IGV sessions, .igv_session.xml / .xml, all standard genomics
formats (bigWig, bigBed, BAM, CRAM, VCF, BED, GFF/GTF, WIG, TDF, FASTA,
2bit...). Stock IGV 2.19.5 workflows continue to work; IGV-X adds robustness
and diagnostics on top.

Install notes

• macOS Apple Silicon (universal build: Apple Silicon; Intel via Rosetta/
  x86_64 build on request).
• Ad-hoc signed: first launch on another Mac may require right-click → Open →
  Open (Gatekeeper). A Developer ID + notarization pass is planned.

Source

• Repository: https://github.com/Micropeptide/IGV-X
• Branch: IGV-X (fork base: upstream 2.19.X, commit e2bcf4200)
• Full diff vs stock IGV: docs/fork-diff.md · docs/changes-vs-igv.md
• What's different: docs/whats-different.md · Build: docs/build.md
• Limitations: docs/limitations.md

IGV-X v2.19.5-igvx.1

IGV-X v2.19.5-igvx.1 — Release Notes

IGV-X is a customized version of IGV built specifically for
micropeptide's research — Arabidopsis
epigenetics, whole-genome bisulfite sequencing (WGBS) methylation analysis,
and large multi-track sessions. It is designed
around those workflows while remaining fully compatible with standard IGV
sessions and genomics file formats.

IGV-X is a robust, modern fork of the Integrative Genomics Viewer (IGV)
(upstream fork base: 2.19.X stable, commit e2bcf4200). It is fully compatible
with standard IGV sessions and genomics file formats, and adds a hardened
chromosome-name resolution layer, large-session performance work, and a
modernized macOS experience.

New in this release

In-app updates (GitHub release channel)

• Help > Check for Updates... — IGV-X checks Micropeptide/IGV-X releases
  on GitHub for a newer version and offers a one-click download of the new
  .dmg installer.
• Optional startup check (off by default): Preferences > Updates (IGV-X) >
  "Check for updates on startup".
• Version comparison understands the vX.Y.Z-igvx.N release scheme.

Highlights of the IGV-X fork

Chromosome-name resolution (top priority)

• Fixes the stock IGV 2.19.5 bigWig NullPointerException on TAIR10 WGBS
  sessions: BBFile.getIdForChr() returning null when hundreds of
  methylation bigWigs use Chr1..ChrM against a RefSeq-aliased genome.
  Missing mappings never NPE — they degrade gracefully and diagnose
  honestly.
• Case-insensitive, alias-aware chromosome resolution across bigWig/bigBed/
  BAM/BED/VCF: Chr1/chr1/CHR1/1/RefSeq accessions/organellar names,
  using genome alias information — never global lowercase conversion,
  never renaming user files.
• Tools > Diagnose Track/Session... shows exactly how each file's
  chromosomes compare to the loaded genome (exact / case-only / alias-only /
  missing), plus index and resource checks.

Large-session performance (~900 bigWigs)

• Bounded loading threads, async track loading with honest progress, viewport
  culling, and caching — no more freezing the UI while a big session loads.

Sessions & files

• Relative session paths by default (relative to the session file).
• Optional .igvx.json companion metadata; sessions still load if it is missing.
• Unified smart Open (files + sessions auto-detected) and recent files.
• Cancel Session Loading — escape a stuck session load and open another.
• Unsaved-session close confirmation.
• Bookmarks & gene-region highlights persisted in the session file.
• Batch track import: File > Open Folder of Tracks... scans subfolders,
  filters by type, multi-select.
• Arabidopsis (tair10) gene lists — DNA methylation core, RdDM pathway,
  small RNA machinery, histone marks & readers, imprinting/DME, flowering time
  (every AGI verified against TAIR10 GTF).

Navigation & region selection

• Trackpad two-finger swipe / Magic Mouse pan (configurable sensitivity),
  without breaking vertical scroll.
• ROI drag-select, multi-track selection (Cmd/Shift-click), data-panel
  selection highlight.
• Configurable default quantitative-track ranges (e.g. min -5 / max 100)
  in Preferences > Tracks > Default Quantitative Range (IGV-X).

Organize tracks by genotype

• Tracks > Organize Tracks by Genotype... — group tracks by genotype with
  per-genotype background tint, then order CG → CHG → CHH inside each group
  with consistent context colors across genotypes. Editable, remembered
  rules; optional auto-organize after session/batch loads.

Export

• High-quality PNG / SVG / PDF export (publication mode, selected tracks
  only, DPI control).

Diagnostics & error recovery

• Exception dedup / rate-limiting (per-type 60 s cooldown) so repeated errors
  don't spam.
• Batch command listener preserved (port 60151: new/genome/load).

macOS app

• Native system menu bar, fullscreen, standard shortcuts, Dock icon,
  window-state memory, accessible dialogs, Retina/HiDPI, information-dense
  dark-friendly UI. App name is IGV-X, own bundle ID, prefs/caches/logs
  separated from stock IGV (~/igvx). Bundled JDK — no Java install needed.

Downloads

• IGV-X-2.19.5-igvx.dmg — shareable installer (drag to Applications)
• IGV-X-2.19.5-igvx.zip — same app, zip form
• SHA256SUMS + version.txt

Compatibility

Standard IGV sessions, .igv_session.xml / .xml, all standard genomics
formats (bigWig, bigBed, BAM, CRAM, VCF, BED, GFF/GTF, WIG, TDF, FASTA,
2bit...). Stock IGV 2.19.5 workflows continue to work; IGV-X adds robustness
and diagnostics on top.

Install notes

• macOS Apple Silicon (universal build: Apple Silicon; Intel via Rosetta/
  x86_64 build on request).
• Ad-hoc signed: first launch on another Mac may require right-click → Open →
  Open (Gatekeeper). A Developer ID + notarization pass is planned.

Source

• Repository: https://github.com/Micropeptide/IGV-X
• Branch: IGV-X (fork base: upstream 2.19.X, commit e2bcf4200)
• Full diff vs stock IGV: docs/fork-diff.md · docs/changes-vs-igv.md
• What's different: docs/whats-different.md · Build: docs/build.md
• Limitations: docs/limitations.md